Comparison between the types for the ages and genders

Questions

  • What are the differences between the type for the different combinations of ages and genders?
  • Do we observe the same changes as globally?

Loads

Libraries and functions

==========================================================================
*
*  Package WGCNA 1.63 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=4
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=4
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


Allowing multi-threading with up to 4 threads.
preparing gene to GO mapping data...
preparing IC data...
preparing gene to GO mapping data...
preparing IC data...
preparing gene to GO mapping data...
preparing IC data...

Data

Stats

Wald padj < 0.05LFC > 0 (Wald padj < 0.05)LFC < 0 (Wald padj < 0.05)
GF VS SPF (F, 8w) 392192 200
GF VS SPF (M, 8w) 161 76 85
GF VS SPF (F, 52w) 738316 422
GF VS SPF (M, 52w) 393145 248
GF VS SPF (F, 104w)2038846 1192
GF VS SPF (M, 104w)2172898 1274

Differentially expressed genes

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”

Comparison of the numbers per ages

Differentially expressed genes

DEG into gene co-expression network

  • White: up-regulated
  • Black: down-regulated
Age F M
8w GF vs SPF GF vs SPF
52w GF vs SPF GF vs SPF
104w GF vs SPF GF vs SPF

GO analysis

Biological process

Dot-plot with the most over-represented BP GO (20 most significant p-values for the different comparison)

Network based on description similarity

F M
8w GF vs SPF GF vs SPF
52w GF vs SPF GF vs SPF
104w GF vs SPF GF vs SPF

GF VS SPF (F, 8w)

scatterplotThree

GF VS SPF (M, 8w)

scatterplotThree

GF VS SPF (F, 52w)

scatterplotThree

GF VS SPF (M, 52w)

scatterplotThree

GF VS SPF (F, 104w)

scatterplotThree

GF VS SPF (M, 104w)

scatterplotThree

Cellular components

Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)

Warning message:
“Removed 7 rows containing missing values (geom_point).”

Molecular functions

Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)

Warning message:
“Removed 7 rows containing missing values (geom_point).”

KEGG pathways

[1] "Note: 11 of 4057 unique input IDs unmapped."
[1] "Note: 11 of 4057 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' 
limit_output extension: Maximum message size of 10000 exceeded with 10090 characters

Pathway graphs available at ../results/dge/type-effect/type_gender_age/over_repr_kegg/

[1] "Note: 11 of 4057 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”
[1] "Note: 11 of 4057 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' 
limit_output extension: Maximum message size of 10000 exceeded with 10090 characters

Pathway graphs available at ../results/dge/type-effect/type_gender_age/under_repr_kegg/

Comparison with Erny results

Protocol: 2 months old female mices (GF vs SPF)

Raw comparison of the results

Detailed comparison

  • Checking the correlation between the counts of Erny and our counts
  • Re-running a DGE analysis on the Erny's raw counts